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We first removed hypothetical and not-significantly-changed (P≥0.05) genes if the P-value is available; then selected a total of 200 genes with maximal fold changes (100 positive, and 100 negative each).
There are many genes with large maximal fold changes between mice but, particularly in adipose tissue, these same genes also have large within-mouse variance, which reduces their statistical significance.
In adipose, 2.6% of all genes exhibit maximal fold changes greater than 2, whereas 0.4-0.6 0.4-0.6 genes show fold changes this large in the other three tissues.
As shown in Figure 5A, the maximal fold changes of MnP1 and MnP2 were relatively small, in that the peak of MnP1 expression was at 15 weeks with a 1.5-fold increase (relative to the expression level at 3 weeks), while MnP2 expression peaked later at 18 weeks with a larger (2.7-fold) increase.
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Genes for which the maximal fold change across the conditions was below 2 were filtered, leaving 1,536 genes (front nodes).
In Figure 1B, we plotted the number of genes by maximal fold change in both the up and down set.
A different picture of the variability in gene expression across tissues emerges when we look at the maximal fold change between mice (Table 1D).
The top five proteins which exhibited the maximal fold change between CCA and BBTD consisted of FAM19A5, MAGED4B, KIAA0321, RBAK, and UPF3B.
S100A12 was significantly (P < 0.01) up-regulated 4 24 h after LPS stimulation with a maximal fold change of 10.6 at 24 h.
Using the fold-change values at the different time points, we performed clustering of the genes by expression profile on a subset of regulated genes (i.e., those with maximal fold change >4).
Briefly this involved calculating the MFC (maximal fold change), i.e. the ratio of the maximum and minimum expression values for all microarrays performed in the experiment, and the CV, i.e. the coefficient of variation.
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